Integrating nanoscale active materials on conductive holey reduced graphene oxide (RGO) framework is an effective strategy to synthesize composite electrode materials for advanced lithium-ion batteries. Herein, a composite of γ-Fe2O3 nanoparticles stabilized by the engineered holes on RGO was successfully synthesized by using a facile in-situ etching route, which exhibited high lithium storage performance. The fundamental insight of its enhancement mechanism was discussed. This work offers a newly route to synthesize the composite of holey RGO confined metal oxide nanoparticles for the applications in lithium ion batteries and beyond.